Currently Chrome supports NPAPI plugins, but they are blocked by default unless the user chooses to allow them for specific sites (via the page action UI). A small number of the most popular plugins are whitelisted and allowed by default. In January 2015 we will remove the whitelist, meaning all plugins will be blocked by default.

In April 2015 NPAPI support will be disabled by default in Chrome and we will unpublish extensions requiring NPAPI plugins from the Chrome Web Store. Although plugin vendors are working hard to move to alternate technologies, a small number of users still rely on plugins that haven’t completed the transition yet. We will provide an override for advanced users (via chrome://flags/#enable-npapi) and enterprises (via Enterprise Policy) to temporarily re-enable NPAPI while they wait for mission-critical plugins to make the transition.

Meanwhile, Linux users still cannot use Chrome on pages that utilize the Java plugin, as it is still using NPAPI, and (as far as I know) any of the "override" flags that allow you to re-enable NPAPI don't work on Linux.